title: Bi-directional ribosome scanning controls the stringency of start codon selection

city: Hangzhou

first: Yuanhui

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

summary: The fidelity of start codon recognition by ribosomes is paramount during protein synthesis. The textbook knowledge of eukaryotic translation initiation depicts 5’→3’ unidirectional migration of the pre-initiation complex (PIC) along the 5’UTR. In probing translation initiation from ultra-short 5’UTR, we report that an AUG triplet near the 5’ end can be selected via PIC backsliding. The bi-directional ribosome scanning is supported by competitive selection of closely spaced AUG codons and recognition of two initiation sites flanking an internal ribosome entry site. Transcriptome-wide PIC profiling reveals footprints with an oscillation pattern near the 5’ end and start codons. Depleting the RNA helicase eIF4A leads to reduced PIC oscillations and impaired selection of 5’ end start codons. Enhancing the ATPase activity of eIF4A promotes nonlinear PIC scanning and stimulates upstream translation initiation. The helicase-mediated PIC conformational switch may provide an operational mechanism that unifies ribosome recruitment, scanning, and start codon selection.

overall_design: Ribo-seq, 40S-seq and eIF3-seq of MEF and HEK293 cells with or without eIF4A1

first: Yifei

last: Gu

first: Longfei

last: Jia

first: Leiming

last: Dong

first: Shu-Bing

last: Qian


title: Gene analysis of tumor cells from mice with the Treg-specific deletion of Blimp1 compared to WT mice (NanoString Cancer)

status: Public on Nov 24 2021

city: Birmingham

first: Jianmei

middle: Wu

last: Leavenworth

state: AL

address: 1600 6th Ave South

department: Neurosurgery, Microbiology

country: USA

institute: University of Alabama at Birmingham

summary:
We observed that mice with the Treg-specific deletion of Blimp1 had delayed and smaller tumor growth associated with the activation of tumor-infiltrating immune effector cells.
To determine what extent disruptions of Treg suppressive activity by a specific deletion of Blimp1 could impact on the tumor, we assessed the gene expression of sorted tumor cells by NanoString analysis.

overall_design: Prdm1fl/flFoxP3YFP-Cre (KO) and FoxP3YFP-Cre (WT) mice were subcutaneously inoculated with B16.OVA at day 0, and intraperitoneally immunized with NP-OVA in CFA at day 0 and NP-OVA in IFA at day 7. When the tumor reached ≤ 1.5 cm3, CD45-live tumor cells were FACS-sorted from the tumors of these mice. RNA was prepared and analyzed using NanoString PanCancer Pathways Panel.

middle: W


title: Gene expression profile of effector Treg cells isolated from spleens and tumors of tumor-bearing mice

type: Expression profiling by high throughput sequencing

summary: A majority of effector Treg cells (eTregs) that are abundant in many types of tumors are marked by the expression of Blimp1. However, the specific impact of Blimp1+ eTregs on, and mechanisms of action within, tumors remain unknown. To better understand the role of Blimp1 in the regulation of eTreg function in the tumor immunity, we profiled the differential gene expression in Blimp1-deficient eTregs compared to WT control eTregs from tumor-bearing mice.

overall_design: Prdm1fl/flFoxP3YFP-Cre (KO) and FoxP3YFP-Cre (WT) mice were subcutaneously inoculated with B16.OVA at day 0, and intraperitoneally immunized with NP-OVA in CFA at day 0 and NP-OVA in IFA at day 7. When the tumor reached ≤ 1.5 cm3, CD45+CD44+YFP+(FoxP3+)CD4+CD3+ Tregs were FACS-sorted from spleens and tumors of these mice. RNA was prepared and sequencing was performed at Genewiz (South Plainfield, NJ) using Ultra-Low Input RNA-Seq Service.


title: Treg cells and Treg-specific deletion of Blimp1

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Gene expression data from CD34+ BMMCs/PBMCs from MPN patients vs. healthy controls

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

country: Germany

institute: University Hospital Aachen

summary:
Philadelphia chromosome-negative myeloproliferative neoplasms (MPN) consist of primary myelofibrosis (PMF), polycythemia vera (PV), essential thrombocythemia (ET) and seconday myelofibrosis (SMF), comprising post-ET-MF(pET-MF) and post-PV-MF(pPV-MF).
In this dataset, we compare the gene expression data of bone marrow or peripheral blood mononuclear cells (BMMCs/PBMCs) of CD34+ cells from MPN patients and healthy donors.

overall_design: 36 samples (6 ET, 11 PV, 9 PMF, 4 secondary MF (SMF) patients and 6 healthy donors) were analyzed

first: Julian

last: Baumeister

first: Tiago

last: Maié

first: Nicolas

last: Chatain

first: Bernd

last: Denecke

first: Barbora

last: Weinbergerova

first: Marcelo A. S.

last: de Toledo

first: Jörg

last: Eschweiler

first: Angela

last: Maurer

first: Jiri

last: Mayer

first: Blanka

last: Kubesova

first: Zdenek

last: Racil

first: Andreas

last: Schuppert

first: Ivan

last: Costa

first: Steffen

last: Koschmieder

first: Tim

middle: H

last: Brümmendorf

first: Deniz

last: Gezer


title: Transcriptomic analysis of E9.5 mouse embryos

city: PULLMAN

first: Liang

last: Zhao

state: WA

address: 100 Dairy Road

institute: Washington State University

summary: Obesity impairs the developmental progress and metabolism of the skeletal muscle. Using scRNA-seq, the initial impacts caused by maternal obesity were revealed at the embryonic stage.

overall_design: Single-cell transcriptomic profiling of mouse embryos on embryonic 9.5 day.

first: Min

last: Du


title: The Keratin 17/YAP/IL6 Axis contributes to E-cadherin Loss and Aggressiveness of Diffuse Gastric Cancer

first: Mengjie

last: Li

address: NO.866 Yuhangtang Road

country: China

summary: The results of High-throughput sequencing revealed that KRT17 was associated with cell apical and cell-cell junction, which is critical for YAP activation.

overall_design: mRNA profiles of NCI-N87 wild type (WT)  gastric cancer cells and KRT17-knockout in NCI-N87 cells.

first: Wei

last: Zhuo


title: Quantitative analysis of wild-type and Pgrmc1 knockout mouse liver transcriptomes

city: Baltimore

first: Peter

last: Espenshade

state: Maryland

address: 725 N Wolfe St., Physiology 107

department: Cell Biology

institute: Johns Hopkins University School of Medicine

summary: The goal of this study is to compare the next generation sequencing-derived liver transcriptome of Pgrmc1 KO mice to wild-type controls to identify differentially expressed genes.

overall_design: Liver mRNA profiles of 8-12 week old male wild type (WT) and Pgrmc1 KO mice pooled by genotype

first: Meredith

middle: R

last: McGuire

middle: J


title: Deep mutational scanning of RNA-binding protein ProQ suggests a mechanism of quality control by protease Lon

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

summary: ProQ has become a paradigm for the emerging family of FinO domain-containing RNA binding proteins. ProQ in Salmonella enterica has been shown to act as a global RNA binding protein as it interacts with a plethora of sRNAs and mRNAs. However, little was known about processes ProQ regulates in Salmonella which have precluded to functionally characterize ProQ in vivo. In here, we show that ProQ represses the utilization of succinate as carbon source. The latter allowed applying deep mutational scanning to ProQ to identify residues within the protein important to its function in vivo. ProQ carries a FinO domain, responsible for RNA binding, as its N-terminal domain fused via a linker to a C-terminal domain with unknown function. Remarkably, residues within both the N-terminal domain and C-terminal domain of the protein are found to be essential for ProQ function. Mutations in the C-terminal lead to non-fuctional variants to regulate succinate utilization but capable to interact with RNA. On the contrary, mutations on the N-terminal domain leave ProQ functionally inactive to regulate ProQ function in vivo and to interact with RNA. Notably, the inability to interact with RNA render ProQ unstable. The latter leads to an active Lon protease mediated degradation suggesting that interaction with RNA represents a control mechanism to modulate ProQ turnover.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Functional residues of ProQ were mapped via deep mutational scanning using the growth phenotype under succinate as a selection pressure for a non-functional protein. A resulting Mutant was used to perform a co-immunoprecipitation (CoIP) experiment to validate its inability to bind RNA.

first: Youssef

last: el Mouali Benomar

last: Vogel


title: RBMS1 regulates lung cancer progression

city: Dalian

first: Wang

last: Yang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary: In order to profile the translation events that were regulated by RBMS1, Ribo-seq was performed on A549 cells which was used to generate RBMS1 stably depleted and overexpressed  lung cancer cells.

overall_design: This study includes a total of 5 ribosome footprint profiling samples, A549_sh1196 and A549_sh1088 was generated as a RBMS1 stably depleted A549 lung cancer cells. A549_R1A was generated as a RBMS1 stably overexpressed A549 lung cancer cells .

first: Yang

last: Yun


title: Reciprocal impacts of telomerase activity and tumor cell differentiation in neuroblastoma tumor biology

city: New York

first: Neal

last: Lue

state: New York

address: 1300 York Ave.

institute: Weill Cornell Medicine


title: Gene expression profiles of  BE(2)N expressing Dn-hTERT

summary:
Purpose: Infection of neuroblastoma cell liner BE(2)N with a retroviral vector that overexpressed Dn-hTERT caused the conversion of these cells from adrenergic morphology to one that resembles mesenchymal cells. During prolonged passage, down-regulation of Dn-hTERT expression caused a reversal in cell morphology (i.e., from mesenchymal to adrenergic cells). The goal of this study is to characterize the transcriptomes of BE(2)N during the morphologic conversion and reversal and determine if the transcription changes are consistent with previously defined ADRN and MES signature genes.
Methods: Total RNA was isolated from parental BE2N cells and cells infected with Dn-hTERT retrovial vector at day 33, day 55, and day 82 post infection. TruSeq stranded mRNA  libraries were prepared and sequenced with paired-end 50 bps on Illumina NovaSeq 6000 by the WCM Genomics Core Facility.  The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.  RNA reads were aligned and mapped to theGRCh37 human reference genome by STAR (Version2.5.2) (https://github.com/alexdobin/STAR) 56, and transcriptome reconstruction was performed by Cufflinks (Version 2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/).  The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM) 57, 58. The fold changes were calculated by directly comparing the FPKM values of samples and controls.
Results: The gene expression changes in Dn-hTERT treated cells were identified. The list of up-regulated and down-regulated genes were found to overlap strongly with previously defined MES and ADRN signature genes, supporting the notion that Dn-hTERT triggers the transcriptional re-programming of ADRN cells into MES cells.
Conclusions: This study demonstrates that the morphologic conversion mediated by inhibition of telomerase in neuroblastoma cells is accompanied by genome wide transcriptional re-programming.

overall_design: mRNA profiles of parental BE(2)N cells and cells infected with Dn-hTERT expressing retrovirus for 33, 55, and 82 days

first: Eun

middle: Y

last: Yu

first: Adrian

last: Tan


title: Gene expression profiles of BrdU-treated BE(2)N during conversion from adrenergic to mesenchymal cell lineages

summary:
Purpose: Treatment of neuroblastoma cell liner BE(2)N is known to convert these cells from adrenergic morphology to one that resembles mesenchymal cells. The goal of this study is to characterize the transcriptomes of BE(2)N during the conversion process and determine if the transcription changes are consistent with previously defined ADRN and MES signature genes.
Methods: BE2N cells were treated with DMSO for 26 days or with 10µM BrdU for 5, 11, 20 and 26 days. Total RNA was isolated with the RNeasy Mini kit (Qiagen), and the quality of the preparations assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies).  TruSeq stranded mRNA  libraries were prepared and sequenced with paired-end 50 bps on Illumina NovaSeq 6000 by the WCM Genomics Core Facility.  The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.  RNA reads were aligned and mapped to theGRCh37 human reference genome by STAR (Version2.5.2) (https://github.com/alexdobin/STAR), and transcriptome reconstruction was performed by Cufflinks (Version 2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/).  The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM). The fold changes were calculated by directly comparing the FPKM values of samples and controls.
Results: The gene expression changes in BrdU-treated BE2N cells were identified through comparison with DMSO-treated control cells. The list of up-regulated and down-regulated genes were found to overlap strongly with previously defined MES and ADRN signature genes, supporting the notion that BrdU triggers the transcriptional re-programming of ADRN cells into MES cells.
Conclusion: This study indicates that the morphologic conversion mediated by BrdU treatment of neuroblastoma cells is accompanied by genome wide transcriptional re-programming.

overall_design: mRNA profiles of BE(2)N cells treated with DMSO for 26 days and with 10 µM BrdU for 5, 11, 20, and 26 days


title: Transcriptomic and metabolomic profiling of Zea mays fed with urea and ammonium

city: Udine

first: Fabio

last: Marroni

address: Via delle Scienze 208

country: Italy

institute: Università di Udine

summary: Plant nutrition takes advantage by the simultaneous presence of more N forms in the rhizosphere. In the last decades the interplay between ammonium and nitrate acquisition systems in roots has been deeply investigated. Although widely used as fertilizers, the occurrence of cross connection between urea and ammonium nutrition has been scarcely studied in plants, especially at molecular level. In a recent paper we provided evidence that maize plants fed with urea and ammonium mix showed a better N-uptake efficiency than plants fed with ammonium or urea alone. To elucidate the molecular mechanism underlying this response, transcriptomic and metabolomic changes occurring in maize plants were investigated. Transcriptomic analyses indicated that several transporters and enzymes involved in N-nutrition were found upregulated by all three N-treatments (AMT1.3, NRT1.1, NRT2.1, GS1, GOGAT, GDH), confirming that urea is a direct source of N for plants. Depending on N-form available in nutrient solution a peculiar response at transcriptomic and metabolomic level was observed, especially after 24 hours of treatment. In comparison to one single N-form, urea and ammonium mix induced a prompt assimilation of N, characterized by an overaccumulation of main amino acids in shoots, and an upregulation of ZmAMT1.1. Moreover even a peculiar modulation of aquaporins, carbonic anydrases, glutamine synthetase, amino aspartate, as well as the glycolysis-TCA cycle was induced in roots by urea and ammonium mix. Depending on N-form available in the external media, even changes in phytohormone’s composition were observed in maize (CKs, ABA, JA); in particular, already after 24 hours of treatment, urea induced the accumulation of trans-zeatin in shoots. Through a multiomics approach, we provide for the first time molecular characterization of maize response to urea and ammonium nutrition. This study paves the way to formulate guidelines for the optimization of N fertilization of crops to improve the N use efficiency in plants and therefore limit N losses in the environment.

overall_design: 12 Samples, 4 conditions (Control, 100% Urea, 50% Urea and 50% N, and 100% N), 3 replicates per condition

first: Sara

last: Buoso

first: Nicola

last: Tomasi

first: Mustapha

last: Arkoun

first: Anne

last: Maillard

first: Sylvain

last: Pluchon

first: Roberto

last: Pinton

first: Laura

last: Zanin


title: Invasive pathobionts in intestinal microbiome contributes to cancer initiation by counterbalancing epithelial antimicrobial responses

city: Taipei

first: Linda

address: 1 Jen-Ai Rd. Sec. 1

country: Taiwan

institute: National Taiwan University


title: Methylation profiling reveals novel molecular classes of rhabdomyosarcoma

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

type: Methylation profiling by genome tiling array

summary: Rhabdomyosarcomas (RMS) represent a family of aggressive soft tissue sarcomas that present in both the pediatric and adult setting. Pathologic risk stratification for RMS has been based on histologic subtype, with poor outcomes observed in alveolar rhabdomyosarcoma (ARMS) and adult-type pleomorphic rhabdomyosarcoma (PRMS) compared to embryonal rhabdomyosarcoma (ERMS). Recent genomic sequencing studies have expanded the spectrum of RMS, with several new molecularly defined entities, including fusion-driven spindle cell/sclerosing rhabdomyosarcoma (SC/SRMS) and MYOD1-mutant SC/SRMS. Comprehensive genomic analysis has previously defined the mutational and copy number spectrum for the more common ERMS and ARMS, as well as revealed corresponding methylation signatures.  In contrast, genetic and epigenetic correlates have not been defined for the rare SC/SRMS or PRMS histologic subtypes.  Herein, we present genomic sequencing, copy number analysis, and methylation profiling of the largest cohort of molecularly characterized RMS samples to date.  We identified two novel methylation subtypes, one having SC/SRMS histology and defined by MYOD1 p. L122R mutations and the other matching adult type PRMS.  Selected tumors from adolescent patients grouped with the PRMS methylation class, expanding the age range of these rare tumors.  Pediatric patients in the MYOD1-mutant group, as well as those clustering with PRMS, appear to have poor overall survival.

overall_design: Herein, we report genomic analysis, including genome-wide methylation profiling, copy number analysis, and next generation sequencing of 154 rhabdomyosarcomas and 4 skeletal muscle controls representing all primary histologic types of both adult and pediatric disease.

first: Brent

last: Orr

first: Michael

last: Clay


title: Invasive pathobionts in intestinal microbiome contributes to cancer initiation by counterbalancing epithelial antimicrobial responses A

summary: Microbiota dysbiosis and mucosa-associated bacteria are involved in colorectal cancer progression. We hypothesized that a time-specific interaction between dysbiotic pathobionts and host responses promote tumor growth. This study aimed to elucidate the dysfunctional host-microbe interplay in colon tumorigenesis by using a time-series metagenomics approach. A transient surge in fecal microbial richness was linked to a unique transcriptome profile in the mouse colon during carcinoma transformation. Monitoring gut microbiome may help identifying the window-of-opportunity to induce tumor regression using bacteria-targeted precision medicine.

overall_design: The gut microbiota in fecal samples was analyzed at various time points in AOM/DSS control mice and those with ABX treatment

middle: C

first: Shu-Chen

last: Wei

first: Yi-Hsuan

last: Li

first: Po-Yu

last: Lin

first: Xin-Yu

last: Chang

first: Jui-Ping

last: Weng

first: Yin-Wen

last: Shue

first: Liang-Chuan

last: Lai

first: Jin-Town

last: Wang

first: Yung-Ming

last: Jeng

first: Yen-Hsuan

last: Ni


title: Invasive pathobionts in intestinal microbiome contributes to cancer initiation by counterbalancing epithelial antimicrobial responses B

last: Yu


title: Single cell RNA sequencing reveals differential cell cycle activity in key cell populations during nephrogenesis

city: Pittsburgh

first: Dennis

last: Kostka

state: PA

department: Developmental Biology

institute: University of Pittsburgh

summary: The kidney is a complex organ composed of more than 30 terminally differentiated cell types that all are required to perform its numerous homeostatic functions. De-fects in kidney development are a significant cause of chronic kidney disease in children, which can lead to kidney failure that can only be treated by transplant or dialysis. A better understanding of molecular mechanisms that drive kidney development is important for designing strategies to enhance renal repair and regeneration. In this study, we profiled gene expression in the developing mouse kidney at embryonic day 14.5 at single cell resolution. Consistent with previous studies, clusters with distinct transcriptional signatures clearly identify major compartments and cell types of the developing kidney. Cell cycle activity distinguishes between the “primed” and “self-renewing” sub-populations of nephron progenitors, with increased expression of the cell cycle related genes Birc5, Cdca3, Smc2 and Smc4 in “primed” nephron progenitors. Augmented Birc5 expression was also detected in immature distal tubules and a sub-set of ureteric bud cells, suggesting that Birc5 might be a novel key molecule required for early events of nephron patterning and tubular fusion between the distal nephron and the collecting duct epithelia.

overall_design: Single cell RNA sequencing pooled cells from two kidneys from a single E14.5 female mouse CD1 embryo.

first: Abha

middle: S

last: Bais

first: Andrew

last: Clugston

first: Jacqueline

last: Ho


title: Transcriptome and proteome dynamics of cervical remodeling in the mouse during pregnancy

city: Dallas

first: Mala

last: Mahendroo

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary:
The transcriptomic patterns that drive cervical softening and ripening in early mid- and late pregnancy were identified in this study. Further we sought to evaluate protein turnover rates with a focus on ECM proteins.
In early pregnancy there is a shift in immune cell and epithelial cell responses at the transcriptional level and an overall slowing down of protein turnover rates. By mid pregnancy transcriptomic patterns indicate there is an increase in extracellular matrix reorganization and by late pregnancy the transcriptional patterns  of early and mid-pregnancy begin to reverse. Protein turnover rates for fibrillar collagen are high in the nonpregnant and pregnant cervix and thus allow for the rapid replacement of mature collagen with poorly crosslinked collagen through pregnancy.

overall_design: RNAseq libraries and proteomic analysis of heavy water labeled proteins was performed using mouse cervices from gestation days 6, 12, 15,18 and nonpregnant.

first: Shanmughasundaram

last: Nallasamy

first: Hector

last: Palacios

first: Rohit

last: Setlem

first: Kelvin

first: Edward

last: Cao

first: Shubha

last: Shankaran

first: Marc

last: Hellerstein


title: Cadmium hijacks the high zinc response by binding and activating the HIZR-1 nuclear receptor

city: Saint Louis

first: Ciro

last: Cubillas Ramirez

state: Missouri

address: 4577 McKinley, Campus Box 8103, 3607 Cancer Research Building

institute: Washington University in St Louis, School of Medicine

summary: Cadmium is an environmental pollutant and significant health hazard that is similar to the physiological metal zinc. In C. elegans high zinc homeostasis is regulated by the HIZR-1 nuclear receptor transcription factor. To define relationships between high zinc homeostasis and the response to cadmium, we identified 145 cadmium-regulated genes. hizr-1 was necessary for activation of a subset of genes, indicating there are at least two mechanisms of cadmium-regulated transcription. Cadmium directly bound HIZR-1, promoted nuclear accumulation of HIZR-1 in intestinal cells, and activated HIZR-1-mediated transcription via the HZA enhancer. Thus, cadmium binding promotes HIZR-1 activity, indicating that cadmium acts as a zinc mimetic to hijack the high zinc response. To elucidate the relationships between high zinc and cadmium detoxification, we analyzed three pathways: the phytochelatin pathway strongly promoted cadmium resistance but not high zinc resistance, the hizr-1 pathway strongly promoted high zinc resistance but not cadmium resistance, and the mek-1/sek-1 pathway promoted resistance to high zinc and cadmium. These studies identify resistance pathways that are specific for high zinc and cadmium as well as a shared pathway.

overall_design: Two Caenorhabditis elegans strains, wild type and a hizr-1 loss-of-function mutant were independtly exposed to toxic cadmium conditions and compared to basal growing conditions. Two biological samples each strain and each condition were used.

first: Brian

last: Earley

last: Cubillas

first: Kurt

last: Warnhoff

first: Raheel

last: Ahmad

first: Alan

last: Alcantar

first: Maximilian

middle: D

last: Lyon

first: Kerry

last: Kornfeld


title: Reversal of age-related deficits in skeletal muscle during disuse and recovery in response to treatment with a secrotome product derived from partially differentiated human pluripotent stem cells

city: Salt Lake City

first: Micah

last: Drummond

state: Utah

address: 520 Wakara Way

department: Physical Therapy and Athletic Training

institute: The University of Utah

summary: We report that the use of high throughput RNA sequencing in C2C12 myotubes induced myotobule hypertrophy and promoted ECM remodeling through alterations in collagen synthesis and turnover.  Transcripts for IGF-binding proteins and Fibromodulin suggest increases in growth and a suppression of myostatin.

overall_design: Examination of fully mature myotubes that were treated with either 4% horse serum differentiation media (DMEM, 4%HS, Pen/Strep) or 4% STEM cocktail media (DMEM, 4% STEM, Pen/Strep).  Tubes were differentiated in 2% HS differentiation media for 5 days. At day 6 each respective treatment was applied to cells for a duration of 24 hours.  After 24 hours cells were collected and RNA isolated and given to the University of Utah Genomics Core for RNA sequencing.

first: Dennis

last: Fix

first: Ziad

last: Mahmassani


title: Invasive Escherichia coli contributes to colon carcinogenesis by suppressing epithelial autophagy: application of phage therapy

first: Linda

last: Yu

summary: Microbiota dysbiosis and mucosa-associated bacteria are involved in colorectal cancer (CRC) progression. However, the temporal changes in commensal-derived pathobionts and host-microbe interactions remain poorly understood. Our study demonstrated that antibiotic (ABX) treatment at a mid phase but not at early or late time points reduced tumor burden in a chemically induced CRC mouse model. A transient surge in fecal microbial richness and emergence of virulence factors were observed at the mid phase of CRC induction. Mouse colonic mucosal tissues were collected before (day 0) and on various days after administration of AOM/DSS (i.e., day 46 as early phase, day 56 as mid phase, and day 66 as late phase), and were analyzed using microarray. Unique profiles of autophagy-related genes were identified in the colonic mucosa during the mid phase, which correlated with the presence of intraepithelial bacteria.

first: Liang-Chuan

last: Lai


title: RNA-Seq analysis of wild-type and ttpA-D450trx mutant D. discoideum amebae

city: Durham

first: Melissa

last: Wells

state: NC

address: 111 TW Alexander Drive

department: LST

institute: NIEHS

summary: In many eukaryotes, mRNAs containing specific AU-rich motifs are regulated by proteins of the tristetraprolin (TTP) family, which bind to these motifs through a tandem zinc finger (TZF) domain.  This binding leads to promotion of subsequent deadenylation and decay, partly through a conserved carboxyl-terminal CNOT1 binding domain.  We explored the physiological role of the single TTP family member (TtpA) expressed in Dictyostelium discoideum. This study shows the effect of a carboxyl-terminal truncation (ttpA-D450trx), which removed the predicted CNOT1 binding domain, evaluated in amebae in growth medium during surface culture. The cells exhibited external and gene expression phenotypes that were very similar to those of two distinct null mutants, raising the possibility that this domain is necessary for TtpA-promoted mRNA decay in this species.

overall_design: Dictyostelium discoideum amebae (strain AX3) were grown in normal growth medium under axenic conditions in plastic flasks until they were approximately 80% confluent.  Four cultures of wild-type cells and four cultures of ttpA-D450trx cells were then frozen and used for RNA extraction and RNA-Seq analysis.

first: Wenli

last: Bai

middle: L

first: Adam

middle: B

last: Burkholder

first: Lalith

last: Perera

last: Kimmel

first: Perry

last: Blackshear


title: Transcriptional profiing of quiescent and lipopolysaccharide-stimulated HIVEP1 deficient pro-monocytic cells

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

summary: In this study, we sought to broaden our understanding of HIVEP1 function in the cellular response to lipopolysaccharide (LPS). The study was done in the context of CRISPR-Cas9 knockdown of HIVEP1 in the pro-monocytic THP1-MD2-CD14 cell line.

overall_design: Examination of RNA expression in THP1-MD2-CD14 cells deficient for HIVEP1 and controls with LPS (100 ng/ml) or medium for 2 or 8 hours. Sample legend: C2MED0h = control cells in RPMI medium (baseline); D2MED0h = HIVEP1 deficient cells in RPMI medium (baseline); C2MED2h = control cells in RPMI medium for 2hours; C2LPS2h = control cells in RPMI+LPS for 2 hours; C2MED8h = control cells in RPMI medium for 8hours; C2LPS8h = control cells in RPMI+LPS for 8 hours; D2MED2h = HIVEP1 deficient cells in RPMI medium for 2hours; D2LPS2h = HIVEP1 deficient cells in RPMI+LPS for 2 hours; D2MED8h = HIVEP1 deficient cells in RPMI medium for 8hours; D2LPS8h = HIVEP1 deficient cells in RPMI+LPS for 8 hours;

middle: P

first: Tom

last: van der Poll


title: RNA-Seq analysis of wild-type and ttpA-C240ins mutant D. discoideum amebae during short-term nutrient deprivation

summary: In many eukaryotes, mRNAs containing specific AU-rich motifs are regulated by proteins of the tristetraprolin (TTP) family, which bind to these motifs through a tandem zinc finger (TZF) domain.  This binding leads to promotion of subsequent deadenylation and decay, partly through a conserved carboxyl-terminal CNOT1 binding domain.  We explored the physiological role of the single TTP family member (TtpA) expressed in Dictyostelium discoideum. This study shows the effect of an insertional mutation in the TZF domain (ttpA-C240ins), which disrupted the TZF RNA binding domain, evaluated in amebae in axenic conditions in growth medium during surface culture, and during short term (2 and 6 hours) nutrient deprivation. RNA-Seq analysis was performed on WT and mutant cells in parallel during this short time course.

overall_design: Dictyostelium discoideum amebae (strain AX3) were grown in normal growth medium under axenic conditions on plastic surfaces until they were approximately 80% confluent.  Three cultures of wild-type cells and 8-9 cultures of mutant cells were then frozen and used for RNA extraction and RNA-Seq analysis.  Other cultures of the same type were changed to nutrient-deficient medium, and harvested after 2 and 6 hours.


title: RNA-Seq analysis of wild-type and ttpA-C231S, ttpA-E236fsx, and ttpA-Y242fsx mutant D. discoideum amebae

summary: In many eukaryotes, mRNAs containing specific AU-rich motifs are regulated by proteins of the tristetraprolin (TTP) family, which bind to these motifs through a tandem zinc finger (TZF) domain.  This binding leads to promotion of subsequent deadenylation and decay, partly through a conserved carboxyl-terminal CNOT1 binding domain.  We explored the physiological role of the single TTP family member (TtpA) expressed in Dictyostelium discoideum. This study shows the effect of three distinct putative null mutations in the ttpA gene on transcript expression in amebae in growth medium during surface culture under axenic conditions. The cells exhibited similar external and gene expression phenotypes, suggesting that they are all null mutants, despite two different types of mutations (two frame shifts and one amino acid substitution).

overall_design: Dictyostelium discoideum amebae (strain AX3) were grown in normal growth medium under axenic conditions in plastic flasks until they were approximately 80% confluent.  Four cultures of wild-type cells and four cultures of each type of mutant cells were then frozen and used for RNA extraction and RNA-Seq analysis.


title: Early-life nasopharyngeal gene expression profiles in the context of the local microbiota and viral infection.

city: Utrecht

first: Wouter

last: de Steenhuijsen Piters

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

summary:
We studied nasopharyngeal gene expression profiles in infants from just after birth until 1 year of age.
We used microarrays to detail the gene expression profiles over time. These gene expression maturation profiles were related to previously generated microbiota data, viral detection data and host and environmental factors (Bosch et al. AJRCCM 2017; SRP093519).

overall_design: For this study, we included gene expression profiles over time from 43 infants.

middle: A

first: Debby

last: Bogaert


title: RNA-Seq analysis of wild-type and ttpA-C240ins mutant D. discoideum amebae in surface and liquid growth

summary: In many eukaryotes, mRNAs containing specific AU-rich motifs are regulated by proteins of the tristetraprolin (TTP) family, which bind to these motifs through a tandem zinc finger (TZF) domain.  This binding leads to promotion of subsequent deadenylation and decay, partly through a conserved carboxyl-terminal CNOT1 binding domain.  We explored the physiological role of the single TTP family member (TtpA) expressed in Dictyostelium discoideum. This study shows the effect of an insertional mutation within the TZF domain (ttpA-C240ins), which creates a null genotype, evaluated in amebae in growth medium during surface culture and liquid culture under axenic conditions.  The mutant cells exhibited severe growth defects and a multinucleate phenotype during liquid culture, but not in surface culture.

overall_design: Dictyostelium discoideum amebae (strain AX3) were grown in normal growth medium under axenic conditions in plastic flasks until they were approximately 80% confluent, or in liquid culture in the same medium until they reached approximately 2 million cells/ml.  Six cultures of wild-type cells and six cultures of ttpA-C240ins cells were then frozen and used for RNA extraction and RNA-Seq analysis.

first: Alan


title: RNA-Seq analysis of wild-type and mutant D. discoideum amebae

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Novel biomarkers for a personalized managemnet of Type II Diabetes [adipose, liver, muscle]

city: Lausanne

first: Ana

last: Rodriguez Sanchez-Archidona

state: Vaud

address: Genopode building - Quartier Sorge

department: CIG

country: Switzerland

institute: University of Lausanne

summary: Quantitative measurement of circulating metabolites may help to identify tissue specific metabolic pathways that are modulated by or causal for a disease condition. The aim of the study was to explore associations between plasma lipid concentrations and gene expression in pancreatic β-cells and insulin target tissues in a mouse model of pre-diabetes to uncover molecular mechanisms and biomarkers of diabetes susceptibility.

overall_design: Murine liver, soleus muscle and visceral adipose tissue transcriptome of three genetically different mouse strains (C57Bl/6J, DBA/2J and BALB/cJ), fed with a high fat diet (HFD) or a regular chow (RC) for different periods of time: 5, 13 and 13 days.

first: Céline

last: Cruciani-Guglielmacci

first: Mark

last: Ibberson

first: Christophe

last: Magnan

first: Bernard

last: Thorens


title: Novel biomarkers for a personalized managemnet of Type II Diabetes


title: Glutamate dehydrogenase (GdhA) of S. pneumoniae is required for high temperature adaptation

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

summary: During its progression from nasopharynx to other sterile and non-sterile niches of its human host, Streptococcus pneumoniae must cope with changes in temperature. We hypothesized that the pneumococcal temperature adaptation is an important facet of pneumococcal in host survival. Here we evaluate the effect of temperature on the phenotype of pneumococcus and the role of glutamate dehydrogenase (GdhA) during thermal stress adaptation associated with virulence and survival. Microarray analysis revealed a significant transcriptional response to temperature changes, affecting the expression of 132 and 119 genes at 34°C and 40°C, respectively, at mid-exponential growth phase relative to at 37ºC. One of the differentially regulated genes was gdhA, which is upregulated at 40°C while downregulated at 34°C relative to 37°C. Mutation of gdhA attenuated the growth, cell size, biofilm formation, pH survival, and virulence factor generation in a temperature dependent manner. Moreover, we identify that both D39 and ΔgdhA strains showed homo-lactic fermentation in glucose, however, ΔgdhA had higher formate production than D39 at all temperatures, which raised the hypothesis that gdhA involves in the regulation of pyruvate formate lyase (pflB) which is activated by catabolite control protein A (CcpA). In silico analysis pointed that a putative CcpA binding site (cre) was found in two proximal regions of -gdhA-coding sequence. The CcpA binding to the putative promoter region of gdhA was confirmed by EMSA. Furthermore, the transcriptional regulation of gdhA by CcpA, was temperature dependent. Finally, ΔgdhA grown at 34°C or 40°C was less virulent in Galleria mellonella infection model, suggesting that GdhA is required for pneumococcal virulence in fluctuating temperatures. These data demonstrated that temperature is an important parameter that affects physiology of S. pneumoniae and GdhA plays a significant role in temperature adaptation.

overall_design: One condition design comparision of two strains including a dye swap

first: Muhammad

last: Afzal

first: Ozcan

last: Gazioglu

first: Hasan

last: Yesilkaya

first: Oscar

last: Kuipers


title: Novel biomarkers for a personalized managemnet of Type II Diabetes [islet]

overall_design: Murine pancreatic islets transcriptome of three genetically different mouse strains (C57Bl/6, DBA/2J and BALB/cJ), fed with a high fat diet (HFD) or a regular chow (RC) for different periods of time: 5, 13 and 13 days.


title: Keloid-specific gene expression profiling for accurate diagnostic and therapeutic applications.

status: Public on Nov 23 2021

city: Gangnam-gu

first: Seok-Hyung

last: Kim

state: Seoul

address: 81, Irwon-ro

department: Department of Pathology

country: South Korea

institute: Samsung Medical Center

summary: Scars are a heterogeneous disease including normotrophic scars, hypertrophic scars, and keloids. Of these lesions, keloids are a distinct subtype from any other type of scar because clinically, it causes pain, itching, or tenderness, causing life discomfort and characteristically irreversible. Therefore, for accurate diagnosis and treatment of keloids, it is essential to identify keloid-specific genes. However, in previous studies, keloids were compared with controls such as scar-free normal skin. In these studies, general scar-related genes were likely to be chosen rather than keloid-specific genes. In this study, we acquired transcriptomic profiles of normotrophic scars, hypertrophic scars, and keloids from formalin-fixed paraffin-embedded human skin samples using high-throughput RNA-sequencing techniques. We compared the transcriptome profile of keloids with those of other scar lesions to select for highly accurate keloid-specific genes and pathways. The results revealed that genes related with several biological processes such as sensory/visual perception are upregulated strongly in keloids, whereas genes related with activation of immune response were downregulated remarkably in keloids. Furthermore, the biological process of extracellular matrix organization was highlighted in both hypertrophic scars and keloids. In conclusion, our study provides insight into the pathogenesis of keloids distinct from other scar lesions as well as potential keloid-specific biomarkers.

overall_design: RNA-seq of normotrophic scar, hypertrophic scar, keloid.

first: M

last: Choi

first: J

last: Lyu

first: E

middle: M

last: Lee

first: Y

last: Oh

first: K

first: S

last: Yeo

first: I

last: Sohn


title: Clinical and biological relevance of the transcriptomic-based prostate cancer metastasis subtypes MetA-C

city: UMEÅ

first: Pernilla

last: Wikström

address: Department of Medical biosciences, Buildning 6M, 2nd floor

department: Medical biosciences, Pathology

institute: Umeå University

summary: Transcriptomic profiling of metastasis tissue samples obtained from prostate cancer patients was performed using Clariom D human arrays.

overall_design: Freshly-frozen bone metastasis samples (n=103) were obtained from spine (n=77), crista (n=22), lymph nodes (n=3) or dermis (n=1), as hormone-naive (n=17), short-term castrated (n=21) or castration resistant (n=65) from a total of 67 patients. RNA was profiled using the Clariom D human arrays (ThermoFisher Scientific Inc., Life Technologies).

first: Elin

last: Thysell

first: Linda

last: Köhn

first: Julius

last: Semenas

first: Helena

last: Järemo

first: Eva

last: Freyhult

first: Marie

last: Lundholm

first: Camilla

middle: T

last: Karlsson

first: Jan-Erik

last: Damber

first: Anders

last: Widmark

first: Sead

last: Crnalic

first: Andreas

last: Josefsson

first: Karin

last: Welén

first: Jonas

last: Nilsson

last: Bergh


title: Human intestinal bitter taste receptors regulate innate immune responses and metabolic regulators in obesity

city: Leuven

first: Kathrin

middle: Ingrid

last: Liszt

address: O&N1 Herestraat 49 – bus 701

country: Belgium

institute: KU Leuven

summary: An expression profiling was conducted to analyse the effect of the bitter tasting compounds denatonium benzoate (DB) or aloin on the transcriptome of human jejunal crypts compared to DMEM-treated crypts. These two bitter compounds are agonists for the human bitter taste receptor TAS2R43. We took advantage of a deletion polymorphism for TAS2R43, that exists in about 33% of the population to compare the effects of the TAS2R43 agonists in obese subjects that express (TAS2R43(+)) or do not express (TAS2R43(-)) TAS2R43.  Primary jejunal crypts from lean (multi-organ donors) or obese (RYGB surgery) subjects were cultured for 24 hours and treated for 4 hours with either DMEM (control) or 1 mM DB or 30 µM aloin. In total 48 mRNA samples were subjected to RNAseq analysis.

overall_design: 6 groups of human jejunal crypts of obese subjects: 1) TAS2R43+, DMEM treatment (n=8), 2) TAS2R43+, 1 mM denatonium benzoate (DB) (n=7), 3) TAS2R43+, 30µM aloin (n=6), 4) TAS2R43-, DMEM treatment (n=5), 5) TAS2R43-, 1 mM DB (n=6), 6) TAS2R43-, 30 µM aloin (n=4)  3 groups of human jejunal crypts of lean subjects with a TAS2R43+ genotype: 1) DMEM treatment (n=4), 1 mM DB (n=4), 5) 30 µM aloin (n=4)

middle: I


title: Transcriptome of CD8+T-cells from C57BL/6 mice in induced tumor-like conditions along with IL-2 and IL-12.

city: Kolkata

first: Debaleena

last: Bhowmik

address: 4 Raja S.C. Mullick Road

department: Cell Biology and Physiology

country: India

institute: CSIR-Indian Institute of Chemical Biology

summary: To study differentially expressed genes via RNA seq analysis of CD8+T-cells from C57BL/6 mice splenocytes treated with the four different conditions: IL-2, IL-2 80%TCM, IL-12 and IL-12 80%TCM. (TCM = Tumor Conditioned Media)

overall_design: RNA seq was performed on CD8+ T-cells from C57BL/6 mice splenocytes after treating with IL-2, IL-2 80%TCM, IL-12 and IL-12 80%TCM.

first: Shilpak

last: Chatterjee


title: Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds

city: Versailles

first: Filipe

last: Borges

address: Route de St-Cyr (RD10)

country: France

institute: Institut Jean-Pierre Bourgin - INRAE

type: Methylation profiling by high throughput sequencing


title: Group-2 Innate Lymphoid Cells Promote Hepatocellular Carcinoma Progression via CXCL2-Neutrophil Induced Immunosuppression

city: Hangzhou

first: Xingyuan

last: Xu

address: No.79 qingchun road

institute: the First Affiliated Hospital, Zhejiang University school of medicine

summary: We report a tissue-derived KLRG1-ILC2s highly expressing CD69 in HCC, which are distinguished from circulating ones from portal vein and peripheral blood. Relief of KLRG1 inhibitory signaling, the HCC-induced ILC2s tend to shape an immunosuppressive tumor microenvironment through CXCL2/neutrophil axis. Furthermore, the abundance of ILC2s in HCC correlated with the recurrence and progression free survival (PFS) of HCC patients indicated ILC2s being an emerging target for HCC immunotherapy.

overall_design: mRNA profiles of ILC2s from HCC and non-tumoral tissues as well as naïve T cells from circulation

first: Longyun

last: Ye

first: Tingbo

last: Liang


title: Investigations into SCAMP5, a candidate lupus risk gene expressed in plasmacytoid dendritic cells

city: Mahasset

first: Andrew

last: Shih

state: NY

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

summary:
Objective: We have investigated the molecular function of SCAMP5, a candidate risk gene for SLE exclusively expressed in plasmacytoid dendritic cells (pDCs) among peripheral leucocytes.
Methods: We tested the independence of the association in SCAMP5 with SLE by performing conditional analyses. We profiled the expression pattern of SCAMP5 among circulating leucocytes at the transcript and protein levels. Using lentiviral vectors, we localised the subcellular distribution of SCAMP5 alongside the interferon secretory pathway. We analysed pDCs for the expression of SCAMP5 and interferon production capacity by SCAMP5 genotype. Finally, we examined pDC-specific SCAMP5 isoforms by total RNAseq analysis and examined for genotype associated quantitative differences therein.
Results: A conditional analysis revealed evidence of an independent genetic association of SCAMP5 with SLE. Among circulating leucocytes, SCAMP5 is uniquely expressed in pDCs at the transcript and protein levels, with main presence in the Golgi apparatus and minor presence at the cell periphery. In live cells, Scamp5 displayed dynamic Golgi cell surface trafficking and localised with the interferon secretory pathway. SCAMP5 did not differ in expression levels in pDCs between genotyped donors; however, a transient interferon secretory defect was noted in pDCs from donors carrying the risk genotype.
Conclusions: SCAMP5 constitutes a novel SLE risk gene on the basis of genomic data and expression in a cell type widely implicated in SLE pathogenesis. While we could not find evidence of quantitative expression differences in SCAMP5 between genotyped donors, SCAMP5 remains an attractive gene to explore given its highly restricted expression pattern and colocalisation with interferon secretion.

overall_design: Investigation of risk versus non-risk genotypes for lupus in pDCs, focused on SCAMP5

first: Mustafa

last: Ghanem

first: Himanshu

last: Vashistha

first: Latanya

middle: N

last: Coke

first: Wentian

last: Li

first: Sun

last: Kim

first: Kim

last: Simpfendorfer

first: Peter

middle: K

last: Gregersen


title: Engineering Modular 3D Liver Culture Microenvironments In Vitro to Parse the Interplay between Biophysical and Biochemical Microenvironment Cues on Hepatic Phenotypes

city: Cambridge

first: Linda

last: Griffith

state: MA

address: 77 Massachusetts Ave

department: Biological Engineering

institute: MIT

summary: In vitro models of human liver functions are used across a diverse range of applications in preclinical drug development and disease modeling, with particular increasing interest in models that capture facets of liver inflammatory status. This study investigates how the interplay between biophysical and biochemical microenvironment cues influence phenotypic responses, including inflammation signatures, of primary human hepatocytes (PHH) cultured in a commercially available perfused bioreactor. A 3D printing-based alginate microwell system was designed to form thousands of hepatic spheroids in a scalable manner as a comparator 3D culture modality to the bioreactor. Soft, synthetic extracellular matrix (ECM) hydrogel scaffolds with biophysical properties mimicking features of liver were engineered to replace polystyrene scaffolds, and the biochemical microenvironment was modulated with a defined set of growth factors and signaling modulators. The supplemented media significantly increased tissue density, albumin secretion, and CYP3A4 activity but also upregulated inflammatory markers. Basal inflammatory markers were lower for cells maintained in ECM hydrogel scaffolds or spheroid formats than polystyrene scaffolds, while hydrogel scaffolds exhibited the most sensitive response to inflammation as assessed by multiplexed cytokine and RNA-seq analyses. Together, these engineered 3D liver microenvironments provide insights for probing human liver functions and inflammatory response in vitro.

overall_design: Gene expression profiles were obtained for hepatocytes cultured for 15 days on either polystyrene or hydrogel scaffolds in a perfused bioreactor, or as static spheroids (PS, PEG, spheroids). Hepatocytes in each scaffold were cultured using a non-inflammatory hepatocyte culture medium (HCM) or a growth-factor and small-molecule supplemented enhanced liver culture medium (eLCM). There are 3 replicates for each scaffold and media culture condition. Code used to generate data can be found at: https://github.com/ajwang3/WangHydrogel-RNASeq

first: Alex

last: Wang

first: Allysa

last: Allen

first: Marianna

last: Sofman

first: Pierre

last: Sphabmixay

first: Ece

last: Yildiz

middle: G


title: Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds [RNA-seq]

first: Filipe

last: Borges

summary: The "triploid block" prevents interploidy hybridizations in flowering plants, and is characterized by failure in endosperm development and function, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed imprinted genes (PEGs) that are up-regulated in the tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed abortion is bypassed in plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early plant growth. We have identified strong suppressor lines showing transgenerational inheritance of hypomethylation in CG context, as well as normalized expression of PEGs. Importantly, differentially methylated loci segregate in the progeny of "epimutagenized" plants, which may allow the identification of epialleles involved in the triploid block response in future studies. Finally, we demonstrate that chemically-induced epimutagenesis allows bypassing interploidy hybridizations in Arabidopsis and interspecific hybridization barriers in crosses between Capsella species, thus potentially emerging as a novel strategy for seed-based breeding of triploids and interspecific hybrids with agronomical interest.

overall_design: RNA sequencing of Arabidopsis seedlings treated with 5-Azacytidine


title: Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds [BiSulfite-seq]

overall_design: Whole-genome bisulfite sequencing of Arabidopsis seedlings treated with 5-Azacytidine


title: Coordinated Maintenance of H3K36/K27 Methylation by Histone Demethylases Preserves Germ Cell Identity and Immortality

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

institute: European Institute of Oncology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Germ cells have evolved unique mechanisms to ensure an everlasting transmission of their genetic and epigenetic information to future generations, whose alteration compromises germ cell immortality. In many instances, epigenetic factors play fundamental roles in these mechanisms. Despite H3K36 and H3K27 methyltransferases shape and propagate over generations a pattern of histone methylation essential for C. elegans germ cell maintenance, the role of respective histone demethylases in this context remains mainly unexplored. Here, we show that jmjd-5 regulates the level of H3K36me2 and H3K27me3, preserves germ cell immortality at high temperature and protects germ cell identity by controlling somatic and germline gene expression. Strikingly, the biological and transcriptional effects of jmjd-5 loss can be hindered by the removal of demethylases for H3K27, indicating that H3K36/K27 demethylases act in a transcriptional framework and promote the accurate balance between H3K36 and H3K27 methylation required for the maintenance of germ cell immortality. Furthermore, we found that in wild-type, but not in jmjd-5 mutant animals, alterations of H3K27 and H3K36 methylation and transcription occur at high temperature, suggesting a role for jmjd-5 in adaptation to environmental changes.

overall_design: Elucidate the role of jmjd-5 in safeguarding germline immortality

first: Nico

last: Zaghet

first: Katrine

last: Madsen

first: Daniel

last: Perez Fernandez

first: Federico

last: Rossi

first: Pier

last: Amendola

first: Ulrich

last: Pfisterer

first: Samuel

last: Demharter

first: Konstantin

last: Khodosevich

first: Anna

middle: E

last: Salcini


title: Microarray profiling analysis of microRNAs expression in Hypertrophic scar

status: Public on Nov 22 2021

city: SHENYANG

first: KAI

last: TAO

state: State

address: Reconstructive and Plastic Surgery, The General Hospital of Northern Theater Command, No. 83, Wenhua Road, Shenhe District

type:
Expression profiling by RT-PCR
Non-coding RNA profiling by array

summary: Excessive repair after burn or trauma will lead to the formation of pathological scar. TGF-β1 is a powerful growth factor after wound healing. It is considered to be a key regulator of HS and various fibrotic diseases. MicroRNAs (miRNAs) can widely participate in the pathophysiological processes of various diseases by participating in post transcriptional gene regulation. At present, there is no research report on miR-361 and hypertrophic scar. This study found that miR-361 in HS is down-regulated. MiR-361 can inhibit the proliferation of HS fibroblasts and promote their apoptosis by inhibiting TGF-β1. Moreover, miR-361 can inhibit the formation of rabbit ear scar by inhibiting the expression of TGF-β1.

overall_design: Three pairs of hypertrophic scar samples and the corresponding  adjacent tissues were collected.


title: Infiltrating B cells and tertiary lymphoid structures in the TME

city: Nanjing

first: wei

last: zhao

state: Jiangsu

address: Gongqingtuan RD No.32

institute: Nanjing first hospital

summary: Single-cell profiling of infiltrating B cells and tertiary lymphoid structures in the TME   of gastric adenocarcinomas

overall_design: Examination of gADC tissue samples and peripheral blood mononuclear cells (PBMCs) sample

first: Wei

last: Zhao


title: Stress modulates Ahi1-dependent nuclear localization of Ten-Eleven Translocation Protein 2

city: Atlanta

first: Yuwen

state: GA

address: 615 Michael ST NE, Suite 305

institute: Emory University

summary: Three Ten-Eleven Translocation (Tet) enzymes are epigenetic regulators of gene expression that promote 5-hydroxymethylcytosine (5hmC) modification of genes. Here, we show that the loss of Tet2 can induce depression-like phenotypes in mice. Paradoxically, using the paradigms of chronic stress, such as chronic mild stress (CMS) and chronic social defeat stress (CSDS), we found that depressive behaviors were associated with increased Tet2 expression but decreased global 5hmC level in hippocampus. We examined the genome-wide 5hmC profile in the hippocampus of Tet2 knockout mice and identified 651 dynamically hydroxymethylated regions, 31 of which overlapped with known depression-associated loci. We further showed that chronic stress could induce the abnormal nuclear translocation of Tet2 protein from cytosol. Through Tet2 immunoprecipitation and mass spectrum analyses, we identified a cellular trafficking protein, Abelson helper integration site-1 (Ahi1), which could interact with Tet2 protein. Ahi1 knockout or knockdown caused the accumulation of Tet2 in cytosol. The reduction of Ahi1 protein under chronic stress explained the abnormal Ahi1-dependent nuclear translocation of Tet2. These findings together provide the evidence for a critical role of modulating Tet2 nuclear translocation in regulating stress response.

overall_design: Examination of genome-wide 5hmC profiles in the hippocampus of WT and Tet2 CKO mice

first: Peng

last: Jin

first: Ziyi

last: Li


title: Innate immune responses in the alveolar space to different formulations of SDI RNA

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: The aim of this experiment was to analyse the innate immune response in alveolar cells after different nanoparticle formulations are delivered intranasally in 50 µl PBS with or without 1 µg Sendai virus Defective Interfering RNA

overall_design: Naive BALB/c mice or mice exposed to influenza B 4 weeks before treatment are given 1 µg of SDI RNA formulated in different nanoparticles intranasally. 4h later, lung alveolar cells are harvested by bronchioalveolar lavage and RNA is extracted for transcriptomic analysis.

first: Michael

last: Schotsaert


title: A trivalent nucleosome interaction by PHIP/BRWD2 is disrupted in neurodevelopmental disorders and cancer

city: Chicago

first: Marc

last: Morgan

state: IL

address: 303 East Superior St, SQI 7-511

institute: Northwestern University

summary: The PHIP chromatin reader protein is mutated in Chung-Jansen syndrome, a neurodevelopmental disorder with autism like symptoms. Here we have characterized the chromatin binding properties of PHIP using a variety of in vitro and in vivo methods.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We have performed ChIP-sequencing of  histone modifications identified as candidate binding sites for the PHIP Tudor and Bromo domains, test to if they co-occur with PHIP occupancy. In addition we have performed RNA-sequencing of PHIP loss-of-function mutants.

first: Michael-C

last: Keogh

first: Ali

last: Shilatifard


title: Gene expression of DREAM complex-related inducible knockouts in HeLa cells

first: Paul

last: Blainey

address: 415 Main Street

institute: Broad Institute

summary: The DREAM complex and interacting proteins (e.g., BMYB and FOXM1) together control cell cycle-dependent gene expression. We identified an unexpected, specific kinetochore defect phenotype after depletion of a DREAM complex member (LIN52) in optical pooled CRISPR knockout screens of essential genes. Here we generated individual doxycycline-inducible Cas9 cell lines expressing lentiviral-integrated sgRNAs targeting LIN52, MYBL2, and FOXM1 to evaluate differential roles in gene expression regulaion.

overall_design: Biological replicates were defined as replicate doxycycline inductions of Cas9 expression. A negative control sgRNA sequence was used that targets a single locus. N=3 biological replicates were performed for each gene target and for the negative control sgRNA (12 total samples).

first: Luke

last: Funk

first: Kuan-Chung

last: Su

first: Iain

last: Cheeseman


title: Signaling pathways, genes and gene networks associated with fat deposition in the tail of different breeds of sheep

city: Tabriz

first: Sana

last: Farhadi

address: Golgasht street

country: Iran

institute: Tabriz University

summary: An essential tissue involved in the development and regulation of lipid metabolism in animals is adipose tissue. The “fat-tail” can supply energy for sheep during migration and winter when a low amount of dry matter intake is available. Tail fat content affects meat quality and varies significantly among the different breeds of sheep. Ghezel (fat-tailed) and Zel (thin-tailed) are two important local Iranian sheep breeds that show different patterns of fat storage. The current study presents the transcriptome characterization of tail fat using RNA-sequencing in order to get a better comprehension of the molecular mechanism of lipid storage in the two sheep breeds. The results of sequencing were analyzed with bioinformatics methods, including differentially expressed genes (DEGs) identification, functional enrichment analysis, structural classification of proteins, protein–protein interaction (PPI), network analysis and module analysis. The results revealed a total of332 DEGs between the Zel and Ghezel breed, with78 up-regulated and 254 down-regulated DEGs in the Zel breed. Identification of differential genes showed that some DEGs, such as IL-6, LIPG, SAA1, SOCS3 and HIF-1α, with the largest fold change had close association with lipid deposition. Also, important lipid storage genes such as FASN and SCPEP1 had high levels of expression. Furthermore, functional enrichment analysis revealed some pathways associated with fat deposition, such as “Fatty acid metabolism”, “Fatty acid biosynthesis” and“HIF-1 signaling pathway”. In addition, structural classification of proteins showed major DEGs in transcription factor classes such as JUNB, NR4A3, FOSL1, MAFF, NR4A1, CREB3L1 and ATF3 were up-regulated in the Zel breed. IL-6, JUNB, and related DEGs were up-regulated in the PPI network.HMGCS1, SUCLA2 and STT3B and related DEGs were down-regulated in the PPI network and had high topology scores as hub genes. This implies the DEGs of these modules are important candidate genes for tail fat metabolism and, therefore, can be further studied.

overall_design: Fat tail mRNA profiles of 7-month old fat and thin tail sheep breeds were generated by deep sequencing, in duplicate using Illumina Hiseq 2000

first: Jalil

last: Shodja

first: Esmail

last: Ebrahimie

first: Karim

last: Hasanpour

first: Abolghasem

last: Mohammadi


title: Deleting DNMT3A in CAR T cells prevents exhaustion and 1 enhances antitumor activity

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

summary: Whole-genome bisulfite sequencing data generated from WT and DNMT3A KO or IL-10 KO CAR T cells.  These data were generate at early (week 1) and later (week 4) time points during in vitro serial stimulation of the CAR T cells, or after infusion into tumor bearing mice.  These data document the DNA methylation changes that are coupled to the functional decline in CAR T cells during their sustained stimulation, and the causal nature of DNMT3A-specific methylation in mediating the functional impairment of the CAR T cells.

overall_design: Total human T cells were transduced with mock or KO specific guide RNAs complexed with CAS.  The gene-edited T cells were then transduce with a vector for expressing a chimeric antigen receptor (CAR).  The WT and KO CAR T cells were then cultured in the presence of tumor cells that express the cognate antigen to stimulate the CAR-T cells.  DNA was extracted from the stimulated CAR T cells at the specified time points and subjected to whole-genome bisulfite sequencing.

first: Brooke

last: Prinzing

first: Caitlin

last: Zebley

first: Christopher

last: Petersen

first: Yiping

last: Fan

first: Alejandro

last: Anido

first: Zhongzhen

last: Yi

first: Phuong

last: Nguyen

first: Haley

last: Houke

first: Matthew

last: Bell

first: Dalia

last: Haydar

first: Charmaine

last: Brown

first: Shannon

last: Boi

first: Shanta

last: Alli

first: Jeremy

last: Crawford

first: Janice

last: Riberdy

first: Jeoung-Eun

last: Park

first: Sheng

last: Zhou

first: Mireya

last: Velasquez

first: Chris

last: DeRenzo

first: Cicera

middle: R

last: Lazzarotto

first: Shengdar

middle: Q

last: Tsai

first: Peter

last: Vogel

first: Shondra

last: Pruett-Miller

first: Deanna

last: Langfitt

first: Stephen

last: Gottschalk

first: Ben

last: Youngblood

first: Giedre

last: Krenciute


title: Role of IFITM3 during primary influenza infection and reinfection

first: Max

last: Chang

summary: WT or IFITM3-KO mice were infected with PR8 H1N1 influenza virus and reinfected with X31 H3N2 influenza virus

overall_design: Mice were challenged sublethally with 0.15LD50 of PR8 H1N1 virus provided by Carles Martinez, which corresponds to 5 plaque forming units (PFU) given intranasally in 50 microliter volume. This is 10^6 dilution of the original stock. Control mice were mock-challenged with diluted allantoic fluid. Four weeks after PR8 infection, mice were reinfected with 1000PFU of X31 H3N2 virus. Lungs were collected, divided in 5 parts and processed at 3 days post infection (DPI) with PR8 H1N1 virus and at 3DPI and 5DPI with X31 H3N2 virus according to the recommendations of the different groups that will process the sample (virus titration, proteomics, lipidomics,metabolomics, transcriptomics).

first: Michael

last: Schotsaert

first: Angela

last: Choi


title: Triple Isozyme Lactic Acid Dehydrogenase Inhibition using GNE-140 in Fully Viable Breast Cancer Cells induces Cytostatic Effects which are not-reversed by exogenous Lactic Acid

status: Public on Nov 20 2021

city: Tallahassee

first: Elizabeth

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

summary: The effects of GNE-140 (50uM), on MDA-MB-231 cells evaluated by whole transcriptome: including mRNAs and long intergenic non-coding RNA transcripts using GeneChip™ Human Gene 2.1 ST Arrays by Affymetrix Inc.

first: Karam

middle: F

last: Soliman


title: Gene expression profile of RAS/RAF–wild-type colorectal cancer patient-derived spheroids

city: Kyoto

first: Makoto

middle: Mark

last: Taketo

state: Kyoto

address: Yoshida-Honmachi, Sakyo

department: Kyoto University Hospital

country: Japan

institute: Kyoto University

summary: We would like to propose a novel parameter that helps predict the chemosensitivity of cancer patients to FGFR inhibitors (FGFRi). Although FGFRi were introduced into the clinical trials on a variety of cancer types, they were found to be particularly efficacious on urothelial cancer and on cholangiocarcinoma for which the FDA had approved several compounds based on clinical studies. The enrollment criteria in such clinical trials were genomic changes in the FGFR genes including amplifications, translocations that caused gene fusions, and point mutations. By scrutinizing the published data on these reports, we have noticed an unresolved issue. Namely, most of these reports showed waterfall plots where tumors of some good fractions of enrolled patients responded well, demonstrating efficacy of the FGFRi. Importantly, however, there were sizable subsets in which tumors did not respond to the FGFRi despite that the patients’ tumors carried the genomic changes that met the enrollment criteria. As already established, both FGFR and EGFR share the downstream signaling pathway of MAPK activation as well as other pathways. Accordingly, it is conceivable that chemotherapeutic inhibition of FGFR alone may leave the MAPK signaling unaffected when the signaling through EGFR is relatively strong. To test this hypothesis, we calculated the FGFR to EGFR mRNA ratio (F/E for short) based on the RNA sequencing data from the Broad Institute Cancer Cell Line Encyclopedia (https://portals.broadinstitute.org/ccle) of cholangiocarcinoma and urothelial cancer cell lines for which FGFRi chemosensitivity had been published in preclinical studies. Because human FGFR has four paralogs FGFR1–4, we first summed up the expression levels of FGFR1–4 mRNAs by adding the read numbers per MB of FGFR paralogs (sumFGFR). To take EGFR expression into consideration, we then divided this number with that of EGFR; F/E. In six biliary tract cancer cell lines tested, two responsive cell lines had higher F/E ratios of 9.5 and 9.0, whereas four non-responsive lines had substantially lower ratios of 0.1–1.8. In 22 urothelial cancer cell lines, four of the five responsive lines showed F/E of 2.8–4.9, whereas 17 non-responsive lines had 0.01–2.7. To obtain further insights into the F/E ratio, we looked into our patient-derived colorectal cancer (CRC)-stem cell lines. Seven (28%) of 25 RAS/RAF-wild type CRC-stem cell lines responded to the pan-FGFRi erdafitinib singly in culture whereas 21 (84%) did respond to erdafitinib in combination with an EGFR inhibitor (erlotinib). The seven singly responsive cell lines showed relatively high F/E ranging 11–207 with the mean of 46, whereas the 18 non-responsive lines had the ratio of 3.5–37 with the mean at 12. These results suggest that F/E can be a useful biomarker also for colorectal cancer chemosensitivity where EGFR expression level can vary widely. Taken together, F/E is another strong predictor of responses to FGFRi that is as useful as the current genomic criteria that are based on the FGFR genomic changes.

overall_design: RNA sequencing data of 25 colorectal cancer spheroid lines, three colorectal cancer whole tissues, and three normal colorectal epithelial spheroid lines

first: Shoichi

last: Kitano

first: Takehito

last: Yamamoto


title: Dynamic intron retention modulates gene expression in the monocytic differentiation pathway

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

summary: We determined the role of intron retention in murine monocyte differentiation

overall_design: Examination of differential Intron retentions in murine monocyte differentiation and functions

first: Wong

last: Justin

first: Song

last: Renhua


title: RNA-sequencing analysis of adult mouse wild type (Prdm16-Mx1-Cko/Cko; +/+) and Prdm16-/- (Prdm16-Mx1-Cko/Cko; Tg/+) Long Term-Hematopoietic Stem Cells (LT-HSC).

city: Frederick

first: Kristbjorn

middle: Orri

last: Gudmundsson

state: MD

address: 1050 Boyles St.

department: MCGP

institute: NCI

summary: Regulation of quiescence is critical for the maintenance of adult hematopoietic stem cells (HSCs). Previous studies by gene disruption during mouse embryonic development have shown that transcription factor gene Prdm16 is important for the generation/maintenance of fetal liver HSCs; however, the underlying mechanisms and the function of Prdm16 in adult HSCs remain unclear. To investigate the role of Prdm16 in adult HSCs, we generated a novel conditional knockout mouse model and deleted Prdm16 in adult mouse hematopoietic system using the interferon inducible Mx1-Cre. Our results show that deletion of Prdm16 leads to a gradual decline of adult HSC numbers and a concomitant increase in the multipotent progenitor (MPP) compartment. Prdm16 deletion in the hematopoietic system following transplantation produced the same phenotype indicating that the defect is intrinsic to the HSCs. This HSC loss was also exacerbated by stress induced by 5-FU injections. Annexin V staining showed no difference in apoptosis between wild type and knockout HSCs. In contrast, BrdU analysis revealed that loss of Prdm16 significantly increases cycling of long-term HSCs (LT-HSCs) with majority of the cells found in the S to G2/M phase. Consistently, RNA-seq analysis of mouse LT- HSCs with and without Prdm16 deletion showed that Prdm16 loss induced a significant decrease in the expression of several known cell cycle regulators of HSCs, among which Cdkn1a and Egr1 were further identified as direct targets of Prdm16. Our results suggest that Prdm16 preserves the function of adult LT-HSCs by promoting their quiescence.

overall_design: Bone marrow was harvested from adult (8-12 week old) Prdm16cko/cko; Mx1-Cre+/+ and Prdm16cko/cko; Mx1-Cretg/+ (5 each genotype) 5 weeks post-pIpC injections for LT-HSCs (Lin-Sca-1+c-Kit+CD48-CD150+) sorting. LT-HSCs were sorted from pooled bone marrow directly into 100 ul RNA lysis buffer (from PicoPure RNA Isolation Kit, Thermo Cat.No. KIT0204) in 3 technical replicates each genotype and stored at -80°C. Low input RNA purification, library generation and Illumina sequencing was performed at Cofactor Genomics (St. Louis, MO).

middle: O

first: Yang

last: Du


title: WhiB4 is required for the reactivation of latent infection of Mycobacterium marinum in zebrafish II

city: Shanghai

first: Chen

last: Lin

address: NO.2005 Songhu road

institute: Fudan university

summary: Granulomas are the pathological hallmark of tuberculosis (TB). In individuals latently infected with Mycobacterium tuberculosis (M. tb), the bacteria are thought to reside within the granulomas in a nonreplicating dormant state due to the lack of oxygen and nutrients. However, a portion of these individuals will develop active TB and little is known on the bacterial mechanisms/factors involved in this process. In this study, we found that WhiB4, an oxygen sensor and a transcription factor, plays a critical role in disease progression and reactivation of Mycobacterium marinum (M. marinum) infection in zebrafish. We show that the whiB4 mutant of M. marinum caused latent infection in adult zebrafish, which is characterized by the stable bacterial loads, constant number of non-necrotized granulomas in fewer organs, and reduced immune responses compared to zebrafish infected with the wild type bacteria or the complemented strain. The mutant bacteria in zebrafish were also less responsive to antibiotic treatments. Moreover, the whiB4 mutant was defective in resuscitation from hypoxia-induced dormancy and that the DosR regulon was dysregulated in the mutant. Taken together, our results suggest that WhiB4 is a major driver of reactivation from latent infection and that WhiB4 is an attractive target for the development of novel therapeutics, which may help to prevent the reactivation of latent infection thereby reducing the incidences of active TB.

overall_design: mRNA profiles of complement and wild type Mycobacteria marinum 1218R in 7 days' hypoxia and 0/0.5/4/24/48hours' reaeration

first: Lu

last: Zhang

first: Jun

last: Liu


title: Side Population Analysis in Clear Cell Renal Cell Carcinoma

city: Toronto

last: Ohh

state: Ontario

address: 661 University Avenue

department: Department of Laboratory Medicine and Pathobiology

country: Canada

institute: University of Toronto

summary: Cancer stem cells have an important role in tumour biology. While their identity in haematological malignancies is clearly defined, stem cell identity remains elusive in some solid tumours. Clear cell renal cell carcinoma (ccRCC) represents the most common form of kidney cancer, but the identity or existence of ccRCC stem cells remains unknown. We aimed to discern their existence using the widely utilised side population approach in ccRCC cell lines. In all cells tested, a well-defined side population was identified, and cell-based assays suggested stem-like properties. However, limiting dilution assays revealed comparable tumour initiating abilities and tumour histology of side and non-side populations, and single cell RNA-sequencing revealed minimal differences between these populations. The results indicate that the side population approach is not sufficient for cancer stem cell discovery in ccRCC.

overall_design: Sorted side population and unsorted whole population of RCC243 cells used for single cell RNA-sequencing

first: Claire

last: Robinson

first: Richard

last: Huang

first: Jalna

last: Meens

first: Scott

last: Yuzwa

first: Laurie

last: Ailles


title: Next Generation Sequencing Facilitates Quantitative Analysis of the effects of CB2 on lung ILC2 Transcriptomes

city: Los Angeles

first: Benjamin

middle: Pierre

last: Hurrell

address: 1450 Biggy Street

department: MMI

country: USA

institute: University of Southern California

summary: CB2 signaling supports secretion of ILC2 effector cytokines ex vivo. Increased ILC2 activation leads to the development of airway hyperreactiviy and lung inflammation. Targeting CB2 signaling may therefore represent a novel therapeutic target to treat asthma.

overall_design: mRNA profiles of sorted mouse lung ILC2s from either WT or CB2 KO mcie were generated by deep sequencing, in triplicate, using a NextSeq 500 (Illumina) system.


title: Antiviral RNA interference in disease vector (Asian longhorned) ticks

last: Li

address: 2005 Songhu Road

institute: Fudan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Tick-borne diseases (TBDs) are the most common illnesses transmitted by ticks, and the annual number of reported TBD cases continues to increase. The Asian longhorned tick, a vector associated with at least 30 human pathogens, is native to eastern Asia and recently reached the USA as an emerging disease threat. Newly identified tick-transmitted pathogens continue to be reported, raising concerns about how TBDs occur. Interestingly, tick can harbor pathogens without being affected themselves. For viral infections, ticks have their own immune systems that protect them from infection. Meanwhile, tick-borne viruses have evolved to avoid these defenses as they establish themselves within the vector. Here, we show in detail that infecting longhorned ticks with distinct arthropod-borne RNA viruses through two approaches natural blood feeding and injection, all induce the production of vsiRNAs. Dicer2-like homolog plays a role in regulating antiviral RNAi responses as knocking down of this gene enhanced viral replication. Furthermore, we demonstrate that tick antiviral RNAi responses are inhibited through expression heterologous VSR proteins in recombinant SINV. We identify both the virus and tick factors are critical components to understanding TBDs. Importantly, our study introduces a novel, in vivo virus-vector-mouse model system for exploring TBDs in the future.

overall_design: 15 virus-derived small RNA from Haemaphysalis longicornis tick infected with different viruses was detected by small RNA-seq.

first: Yan

last: Xu

first: Zhengwei

last: Zhong

first: Yanxin

last: Ren

first: Liting

last: Ma

first: Zhi

last: Ye

first: Chuang

last: Gao

first: Jingwen

last: Wang


title: Role of diverse NS1 influenza segments in the infection of human bronchial epithelial cells

first: Max

last: Chang

summary: Transcriptome comparison of influenza infection with diverse NS1 sequences with a common H5N1 background.

overall_design: Viral infections were carried out in duplicate, with a mock infection as control. The Vietnam sequence also serves as a reference.

first: Raquel

last: Munoz

first: Elena

last: Moreno Del Olmo


title: Recombinant erythroid Kruppel-like factor fused to GATA1 up-regulates delta- and gamma-globin expression in erythroid cells primary adult human erythroid progenitor cells

status: Public on Nov 21 2021

city: Bethesda

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

summary: The EKLF-GATA1 fusion proteins enhances δ-globin expression through interaction with the GATA1-binding motif of the δ-globin promoter. The goal this study is to find if  the fusion proteins could have a different pattern of chromatin occupation from GATA1.  The alignment of ChIP-Seq peaks revealed that the binding peaks of EKLF-GATA1 fusion proteins at the β-globin cluster overlapped substantially with those of GATA1 (A), suggesting that these proteins may associate with chromatin in a similar configuration within the β-globin locus and LCR. Global analysis of EKLF-GATA1 and GATA1 ChIP-seq data sets also revealed a significant number of shared sites on the genomic scale.

overall_design: CD34+ cells transduced with EKLF, GATA1, or EKLF-GATA1 proteins, in quadruplicate.

first: Griffin

middle: P

last: Rodgers

first: Jianqiong

last: Zhu


title: Liver Transcriptomes of Non-alcoholic Steatohepatitis in Mice

first: Xiang

last: Liping

address: 180 Fenglin Road, Xuhui, Shanghai

summary: Non-alcoholic steatohepatitis (NASH), has emerged as a major cause of liver failure and hepatocellular carcinoma. Although decades of studies have improved our understanding of its pathophysiology, the molecular mechanisms are still incompletely understood. In the current study, using a diet-induced mouse model of NASH, we performed RNA Sequencing analysis to reveal molecular features of NASH progression. As a result, we obtained hepatic genome-wide mRNA expression in the livers from two groups of mice (NASH versus Normal).Using FDR < 0.01 and fold change > 2 as the threshold, we identified 1745 differentially expressed genes (DEGs) in the livers of NASH mice relative to the normal control mice, of which 1484 up-regulated and 261 down-regulated. The top 5 up-regulated genes included the genes encoding for Trem2, Lcn2, Ephb2, Mmp12 and Sprr1a.Gene ontology (GO) analysis showed that the up-regulated genes in NASH mice were mainly enriched in biological processes such as response to biotic stimulus, regulation of immune system process and myeloid leukocyte activation, while down-regulated genes were related to organonitrogen compound biosynthetic process and organic acid metabolic process.KEGG pathway enrichment results showed that up-regulated genes were mainly enriched in toll like receptor signaling, regulation of actin cytoskeleton, leukocyte transendothelial migration, chemokine signal pathway as well as cytokine and cytokine receptor interaction, while down-regulated gene clusters were mainly enriched in and steroid biosynthetic as well as glycine serine and threonine metabolism.Meanwhile, as expected, genes involved in hepatic lipogenesis (Srebp-1c, Fasn and Scd-1), lipid absorption (CD36), inflammation (Tnfa, IL1b and Ccl2), and fibrosis (Col1a1, Tgfb1 and Mmp13), are up-regulated in NASH mice.Our study may help to uncover  NASH molecular basis and provide therapeutic targets for its treatment.

overall_design: Liver mRNA profiles of NASH and Normal mice

first: Liping

last: Xiang

first: Yunchen

last: Luo

first: Yiling

last: Qian

first: Lu

last: Yan


title: TP53 wild type/PPM1D mutant diffuse intrinsic pontine gliomas are sensitive to a MDM2 antagonist

city: Durham

first: Matthew

last: Waitkus

address: 203 Research Drive, Medical Science Research Building 1, Room 181A

institute: Duke University

summary: this study demonstrates the pre-clinical efcacy potential of RG7388 in the TP53 wild type/PPM1D mutant DIPG subgroup in the TP53 wild-type/PPM1D mutant DIPG subgroup mutant DIPG subgroup

overall_design: Transcriptome profiling of DIPG-007 wilde-type and TP53 knockout isogenic cell lines  treated with RG7388

first: Cheng

last: Xu

first: Heng

last: Liu

first: Christopher

middle: J

last: Pirozzi

first: Lee

middle: H

last: Chen

first: Paula

last: Greer

first: Bill

last: Diplas

first: Liwei

last: Zhang

middle: S

first: Yiping

last: He

first: Hai


title: A Functional Role of OLIG2 in Tumor Heterogeneity of MYC-amplified Medulloblastoma

city: Washington

first: Yanxin

last: Pei

state: DC

address: 111 Michigan Ave NW

department: Center for Cancer and Immunology

institute: Children's National Medical Center

summary: To study how radiation alters the different types of cells during tumor recurrence in high-risk MYC-amplified MB, we performed scRNA-seq using the 10X Genomics scRNA-seq platform to compare the primary untreated tumors, residual tumors immediately following radiotherapy, and the spontaneously recurrent tumors 7-8 weeks post-irradiation using OLIG2-high MB002 PDX. We found that:1, the variety of cell types demonstrated that the MYC-amplified MB PDX tumors were heterogenous communities, comprising diverse cell types in a broad range differentiation states and developmental trajectories, and included the host-derived cells of the tumor microenvironment; 2, Radiation-induced transient changes in cellular heterogeneity that resolved as tumor recurred; 3, Recurrent tumors showed global changes in gene expression compared to primary tumors

overall_design: We dissected tumors from the brains of 3 replicate PDX mice from 3 conditions, primary untreated tumors, residual tumors immediately following radiotherapy, and the spontaneously recurrent tumors 7-8 weeks post-irradiation using OLIG2-high MB002 PDX.  We dissociated the samples, and FAC-sorted the human cells using the mCherry marker. We then processed the sorted cells using the 10X Genomics scRNA-seq platform and sequenced the resulting libraries.

first: Zhenhua

first: Daniel

last: Malawsky

first: Timothy

last: Gershon


title: mRNA profiling after TAC/Sham surgery in NRON KO/wt mice

city: Hannover

first: Julia

last: Leonardy

address: Carl-Neuberg-Straße 1

department: IMTTS

country: Germany

institute: Medical School Hannover

summary: The long-non coding RNA NRON is enriched in cardiomyocytes where it localizes in the nucleus. Unexpectedly, NRON-overexpression in a transverse aortic constriction-induced hypertrophy mouse model exacerbated hypertrophy, whereas cardiomyocyte-specific NRON-deletion attenuated cardiac hypertrophy, thereby suggesting a novel regulatory role of NRON in the heart.

overall_design: To gain insight into molecular processes affected by NRON KO in cardiac hypertrophy, we performed RNA sequencing of heart samples from WT and NRON KO mice 6 weeks after Sham and TAC surgery. Global gene expression was compared between three groups: WT mice exposed to Sham surgery (Sham WT), WT mice exposed to TAC surgery (TAC WT) and NRON KO mice exposed to TAC surgery (TAC KO).

first: Christian

last: Bär

first: Thum

last: Thomas


title: RNA-seq of CPEB4-overexpressed LoVo cells

status: Public on Nov 19 2021

first: Shenglin

last: Huang

address: 270 Dongan

country: China

summary: NOT PROVIDED; REQUESTED

overall_design: CPEB4 overexpression was introduced into LoVo cells via lenti-virus system. Then total RNAs were subjected to RNA isolation and RNA-seq analyses were generated by deep sequencing using Illumina Hiseq.

first: Qifeng

last: Wang

first: Yingjun

last: Zhao


title: Human Rhinovirus Infection of the Respiratory Tract Affects Sphingolipid Synthesis

city: New York

first: Simone

last: Caielli

address: 413 E 69th Street

department: Department of Pediatrics

institute: Weill Cornell Medicine

summary: We report the application of bulk RNA sequencing to RNA extracted from lung tissue and magnetic bead isolated EpCAM+ lung epithelial cells and CD45+ lung immune cells from mice.  Heterozygous serine palmitory transferase subunit 2 , Sptlc2+/- (SPT) and Sptlc2+/+ controls (WT) mice were included. Differential gene expression analysis reveals genes within the sphingolipid synthesis pathway are similarly expressed in the lung and lung epithelial cells of RV infected WT mice and SPT mice (both infected and uninfected).

overall_design: mRNA profiles from lung tissue, lung EpCAM+ epithelial cells and lung CD45+ immune cells collected from 8 week old WT and SPT mice, 24 hours after after intrasal innoculation with human rhinovirus (HRV)or PBS

first: Stefan

last: Worgall

first: Emily

last: Wasserman

first: Uthra

last: Balaji

first: Jinghua

last: Gu


title: Bulk RNA-seq analysis of the effects of ECHS1 knockdown on cardiomyocyte transcriptome

city: Chengdu

first: Xiaoqiang

last: Tang

address: Renminnan Road

institute: Sichuan University

summary: Short-Chain Enoyl-CoA Hydratase Mediates Histone Crotonylation and Contributes to Cardiac Homeostasis

overall_design: Neonatal rat cardiomyocytes were transfected with siECHS1 or siNC for 48 hours, total RNA was collected and subjected to RNA sequencing

first: De-Pei

last: Liu


title: circEPS15 overexpression in hepatocellular carcinoma modulates tumor invasion and migration [qRT-PCR validation]

city: Beijing

first: Yuntao

last: Bing

address: No.49 Huayuan North Road

department: Department of General Surgery

institute: Peking University Third Hospital

summary:
Background: Hepatocellular carcinoma (HCC) is one kind of the leading causes of cancer-related deaths in the world. Recent evidence indicates that circular RNAs (circRNAs) play important roles in tissue development, gene transcription, signal regulation and tumorigenesis. However, whether circRNAs are involved in HCC progression and encode functional proteins remains largely unknown.
Methods: circRNAs microarrays were performed using pathologically diagnosed HCC samples and paired adjacent normal liver tissues. Cell invasion, migration, cycle, and apoptosis post circRNA overexpression were measured using a transwell culture system, a wound healing assay, and flow cytometry. Full-length, mutated, and truncated sequences of circEPS15 with a FLAG tag were inserted into a circular expression vector. Western blotting was used to confirm circEPS15 expression and the requirement of internal ribosomal entry site (IRES) elements within the circRNA. The miRNA and mRNA expression profiles were obtained by analyzing data retrieved from The Cancer Genome Atlas (TCGA) database. We then constructed a ceRNA network ofcircEPS15, miRNAs, and mRNAs.
Results: The expression of circEPS15 was downregulated in HCC tissues, and the survival curves showed that low circEPS15 levels were associated with poor overall survival in HCC patients. Overexpression of circEPS15 suppressed tumor invasion and migration by inhibiting the TJP1/CDH2/VIM signaling pathway and retarded cell cycle progression, yet had no effect on cell apoptosis. ceRNA analysis and qRT-PCR results suggest a possible circRNA (circEPS15)-miRNA-mRNA network in HCC. The spanning junction open reading frame in circEPS15 driven by IRES encoded a novel protein.
Conclusions: Endogenous circEPS15 plays a novel role in repressing HCC through the ceRNA network and encoding a functional protein.

overall_design: A total of 40 HCC tissues and matched adjacent nontumor tissues were obtained from patients who underwent surgery in the Third Hospital, Peking University. Total RNA from each sample was pooled prior to quantitative RT-PCR.

first: YUNTAO

last: BING

first: DIANRONG

last: XIU

first: CHUNHUI

last: YUAN

first: BIN

last: JIANG

first: MAOLIN

last: TIAN

first: GANG

last: LI


title: ARID1B is a Dosage-sensitive Regulator of Polycomb Repressive Complex Distribution and HOX Gene Regulation in Patient-derived Neural Progenitors

city: Stanford

first: Andrey

last: Krokhotin

address: 279 Campus Drive W

institute: HHMI

summary: Recent unbiased exome and whole-genome sequencing studies have identified ARID1B (originally BAF250b) as the most frequently mutated gene in human de novo neurodevelopmental disorders and a high confidence autism gene. ARID1B is a subunit of the multimeric SWI/SNF or Brg/Brahma-Associated Factor (BAF) ATP-dependent chromatin remodeling complex. Studies of Arid1b+/- mice as well as other BAF subunit mutants have found defects in neural progenitor proliferation and activity-dependent neuronal dendritogenesis; however, to date, the molecular impact of ARID1B mutations on the human neural lineage has not been investigated. Remarkably, ARID1B is required for expression of HOX genes, including anterior HOX genes necessary for brain development. Despite the high homology with ARID1A and the fact that ARID1A is expressed at about 3-fold higher levels, it is unable to compensate for heterozygous loss of ARID1B. These changes in gene expression were paralleled by dosage-sensitive altered deposition of histone H3 lysine-27 trimethylation (H3K27me3) and histone H2A lysine-119 ubiquitination (H2AK119ub) indicating that an evolutionarily conserved pathway of HOX gene regulation underlies the neurodevelopmental defects accompanying ARID1B haploinsufficiency. Using FIRE-Cas9, we show that the unmutated ARID1B allele can be activated to near normal and potentially therapeutic levels.

overall_design: RNA-seq, ATAC-seq, H3K27me3 and H2AK119ub profiles of human patient-derived wild type (WT), ARID1B+/- and ARID1B-/- neural progenitors

first: Esther

last: Son


title: Nrf2-regulated L-2-hydroxyglutarate sensitizes erythroid cells to ferroptosis in sickle cell disease

city: Augusta

first: Xingguo

last: Zhu

state: Georgia

department: Cancer Center

institute: Augusta University

summary: SCD had hemolysis with elevated levels of heme and iron, which induced ferroptosis. Here, we found Nrf2 knockout in SCD mice accumulated the levels of the metabolite L-2-hydroxyglutarate (L2HG), which impaired ferroptosis stress response to exacerbate SCD symptom. Mechanistically, L2HG was found to regulate the expression of genes involved in the iron and heme metabolism via histone epigenetic hypermethylation. Our findings indicate an important role of Nrf2/L2HG in SCD for ferroptosis response.

overall_design: Comparison of spleen erytrhoid cells transcriptome in sickle cell disease Nrf2 WT (3 samples) and Nrf2 KO mice (3 samples) at 2-3 month of age.

first: Caixia

last: Xi

first: Junfeng

last: Pang


title: Transcriptomic profiling of an oceanic diatom adapted to Cu deficiency

city: Montreal

first: Liangliang

last: Kong

state: Quebec

address: 1205 Docteur Penfield

department: Biology

institute: McGill

summary: Enhanced vertical stratification brought about by warming of the ocean surface is expected to reduce vertical circulation and nutrient input with knock-on effects for phytoplankton.  Increased nutrient limitation is one predicted outcome, but the response of phytoplankton is uncertain because long-term adaptation to nutrient limitation has not been studied.  We used Cu as a model catalytic nutrient to explore the adaptive response of an oceanic diatom to continuous nutrient deprivation. Thalassiosira oceanica was maintained under Cu-limiting and sufficient conditions for more than 2000 generations and the evolved populations evaluated for physiological traits in a reciprocal transplant experiment.  Adaptation to low Cu concentration increased Cu use efficiency, so that under Cu-limiting conditions T. oceanica maintained significantly faster rates of net C assimilation and growth than the control and ancestral populations.

overall_design: Examination of low Cu-adapted (LCuA) and control Cu-adapted (CCuA) Thalassiosira oceanica cells, in triplicate, using illumina HiSeq 3000


title: A miRNA Cassette Reprograms Smooth Muscle Cells into Endothelial Cells

city: Boston

first: Mark

last: Feinberg

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's

summary: We report the differentially expressed genes in CASMCs, HUVECs, and induced EC (iECs).

overall_design: RNA-Seq analysis was performed in CASMCs, HUVECs, and induced EC (iECs) using standard library construction and Illumina HiSeq2500 V4 2x100 PE (Genewiz, South Plainfield, NJ).

first: Michael

last: McCoy

first: Daniel

last: Pérez-Cremades

first: Nathan

last: Belkin

first: Wenhui

last: Peng

first: Bofang

last: Zhang

first: Akm

last: Khyrul Wara

first: Rulin

last: Zhuang

first: Henry

last: Cheng

middle: W

first: Jingshu

last: Chen

first: Madhur

last: Sachan


title: RNA sequencing of LINC02015 knockdown in human aortic smooth muscle cells

status: Public on Nov 18 2021

first: Qiang

last: Ji

address: 180 Fenglin Rd.

institute: Zhongshan Hospital Fudan University

summary: This study was designed to explore the role of LINC02015 in regulating biological behaviors of vascular smooth muscle cells (VSMCs) and investigate the interacting targets of LINC02015 with high-throughput techniques and bioinformatics analysis. Total RNA was extracted from cells using Trizol Reagent (Invitrogen, Carlsbad, USA). RNA concentration was measured by NanoDrop ND-1000. RNA samples were reversely transcribed to cDNA library using the SuperScript III Reverse Transcriptase kit (Invitrogen). The gene expression profile was acquired by RNA sequencing. The differentially expressed RNAs were statistically significant with a change of >2.0 or <2.0-fold with P<0.05.


title: Immunization with two heterotypic influenza hemagglutinins by time difference effectively produces broadly binding antibodies against heterotypic influenza virus

city: Yokohama

first: Takashi

last: Watanabe

address: 1-7-22, Suehiro, Tsurumi

institute: RIKEN

summary: Broadly protective antibodies against highly variable pathogens are very important for design of vaccines and therapeutics. We report that by administering two heterotypic influenza hemagglutinins (HAs) to mice by time difference, monoclonal antibodies can be obtained that bind strongly to both heterotypic influenza HAs. More interestingly, it was able to bind widely to the untreated subtype of HA.

overall_design: Examination of antibodies produced when mice are immunized with two types of HA (H1 and H2).

first: Osamu

last: Ohara